Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6NG5Z

Calculation Name: 3ZLA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZLA

Chain ID: A

ChEMBL ID:

UniProt ID: P16495

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2853162.952343
FMO2-HF: Nuclear repulsion 2760515.655339
FMO2-HF: Total energy -92647.297004
FMO2-MP2: Total energy -92920.361359


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-1:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-1.1240.963-0.013-1.186-0.8880.005
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.018
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A1MET00.003-0.0083.863-0.1451.942-0.013-1.186-0.8880.005
4A2ILE0-0.016-0.0087.034-0.083-0.0830.0000.0000.0000.000
5A3GLU-1-0.939-0.95110.678-0.549-0.5490.0000.0000.0000.000
6A4LEU0-0.053-0.03713.896-0.006-0.0060.0000.0000.0000.000
7A5GLU-1-0.909-0.94517.133-0.410-0.4100.0000.0000.0000.000
8A6PHE0-0.047-0.03720.4480.0290.0290.0000.0000.0000.000
9A7HIS0-0.0100.00024.219-0.015-0.0150.0000.0000.0000.000
10A8ASP-1-0.920-0.95327.660-0.159-0.1590.0000.0000.0000.000
11A9VAL0-0.026-0.02331.357-0.002-0.0020.0000.0000.0000.000
12A10ALA0-0.021-0.01634.1620.0040.0040.0000.0000.0000.000
13A11ALA00.0440.02337.9190.0050.0050.0000.0000.0000.000
14A12ASN0-0.067-0.03839.2200.0050.0050.0000.0000.0000.000
15A13THR00.0260.02838.7300.0010.0010.0000.0000.0000.000
16A14SER0-0.013-0.00941.7410.0040.0040.0000.0000.0000.000
17A15SER0-0.013-0.01344.063-0.002-0.0020.0000.0000.0000.000
18A16THR0-0.018-0.00942.921-0.003-0.0030.0000.0000.0000.000
19A17PHE00.0560.03944.9390.0020.0020.0000.0000.0000.000
20A18ASP-1-0.820-0.91146.756-0.054-0.0540.0000.0000.0000.000
21A19PRO0-0.008-0.00450.114-0.002-0.0020.0000.0000.0000.000
22A20GLU-1-0.808-0.87951.247-0.043-0.0430.0000.0000.0000.000
23A21VAL00.0210.00551.9790.0010.0010.0000.0000.0000.000
24A22ALA00.0130.01348.7830.0000.0000.0000.0000.0000.000
25A23TYR0-0.055-0.05150.6880.0000.0000.0000.0000.0000.000
26A24ALA00.0070.00153.1470.0010.0010.0000.0000.0000.000
27A25ASN00.0190.01749.1530.0020.0020.0000.0000.0000.000
28A26PHE00.005-0.00349.8130.0000.0000.0000.0000.0000.000
29A27LYS10.8630.91251.8730.0410.0410.0000.0000.0000.000
30A28ARG10.8910.95252.7850.0580.0580.0000.0000.0000.000
31A29VAL00.0000.01250.9890.0010.0010.0000.0000.0000.000
32A30HIS00.0400.00947.6630.0030.0030.0000.0000.0000.000
33A31THR0-0.118-0.07153.0640.0020.0020.0000.0000.0000.000
34A32THR00.0010.00255.8480.0020.0020.0000.0000.0000.000
35A33GLY00.0160.02056.2780.0020.0020.0000.0000.0000.000
36A34LEU0-0.050-0.01854.0170.0000.0000.0000.0000.0000.000
37A35SER00.032-0.00557.0430.0020.0020.0000.0000.0000.000
38A36TYR00.024-0.04157.938-0.001-0.0010.0000.0000.0000.000
39A37ASP-1-0.794-0.87958.698-0.026-0.0260.0000.0000.0000.000
40A38HIS00.0550.03954.081-0.001-0.0010.0000.0000.0000.000
41A39ILE00.0240.01753.702-0.001-0.0010.0000.0000.0000.000
42A40ARG10.8580.91954.6300.0240.0240.0000.0000.0000.000
43A41ILE0-0.027-0.01051.1100.0010.0010.0000.0000.0000.000
44A42PHE0-0.027-0.00747.1520.0000.0000.0000.0000.0000.000
45A43TYR00.017-0.01350.2240.0000.0000.0000.0000.0000.000
46A44ILE0-0.043-0.01152.0720.0010.0010.0000.0000.0000.000
47A45LYS10.8570.90548.3940.0280.0280.0000.0000.0000.000
48A46GLY00.0590.04447.297-0.002-0.0020.0000.0000.0000.000
49A47ARG10.9450.96845.5750.0180.0180.0000.0000.0000.000
50A48GLU-1-0.791-0.87544.001-0.028-0.0280.0000.0000.0000.000
51A49ILE00.0110.03042.677-0.003-0.0030.0000.0000.0000.000
52A50LYS10.9760.98240.7940.0410.0410.0000.0000.0000.000
53A51THR0-0.005-0.01339.169-0.004-0.0040.0000.0000.0000.000
54A52SER0-0.049-0.04937.938-0.003-0.0030.0000.0000.0000.000
55A53LEU00.0330.02537.611-0.003-0.0030.0000.0000.0000.000
56A54ALA00.006-0.00635.288-0.005-0.0050.0000.0000.0000.000
57A55LYS10.9140.95433.3780.0370.0370.0000.0000.0000.000
58A56ARG10.8810.95832.4450.0610.0610.0000.0000.0000.000
59A57SER00.0250.00427.944-0.003-0.0030.0000.0000.0000.000
60A58GLU-1-0.825-0.90829.992-0.101-0.1010.0000.0000.0000.000
61A59TRP00.0810.03031.4950.0100.0100.0000.0000.0000.000
62A60GLU-1-0.860-0.91333.199-0.097-0.0970.0000.0000.0000.000
63A61VAL0-0.007-0.00336.3750.0010.0010.0000.0000.0000.000
64A62THR0-0.016-0.00538.7550.0020.0020.0000.0000.0000.000
65A63LEU0-0.0040.00142.3900.0030.0030.0000.0000.0000.000
66A64ASN00.024-0.01044.749-0.002-0.0020.0000.0000.0000.000
67A65LEU0-0.0300.00447.7190.0030.0030.0000.0000.0000.000
68A66GLY00.011-0.00950.5380.0020.0020.0000.0000.0000.000
69A67GLY0-0.023-0.01752.6840.0000.0000.0000.0000.0000.000
70A68TRP00.0510.04150.732-0.001-0.0010.0000.0000.0000.000
71A69LYS10.9100.95045.7760.0570.0570.0000.0000.0000.000
72A70ILE00.0150.00746.431-0.001-0.0010.0000.0000.0000.000
73A71THR00.0000.00940.7880.0020.0020.0000.0000.0000.000
74A72VAL0-0.078-0.03441.1170.0020.0020.0000.0000.0000.000
75A73TYR00.007-0.00436.7580.0000.0000.0000.0000.0000.000
76A74ASN0-0.068-0.03734.3180.0100.0100.0000.0000.0000.000
77A75THR00.012-0.01934.516-0.005-0.0050.0000.0000.0000.000
78A76ASN0-0.128-0.05835.7370.0010.0010.0000.0000.0000.000
79A77PHE00.0150.02227.4680.0050.0050.0000.0000.0000.000
80A78PRO0-0.041-0.03729.379-0.005-0.0050.0000.0000.0000.000
81A79GLY00.0160.00527.381-0.001-0.0010.0000.0000.0000.000
82A80ASN0-0.0140.01028.122-0.019-0.0190.0000.0000.0000.000
83A81ARG10.8990.95430.8090.0830.0830.0000.0000.0000.000
84A82ASN0-0.021-0.02331.146-0.002-0.0020.0000.0000.0000.000
85A83ASN00.0350.04030.349-0.010-0.0100.0000.0000.0000.000
86A84PRO00.003-0.00932.3550.0090.0090.0000.0000.0000.000
87A85VAL0-0.020-0.01135.570-0.002-0.0020.0000.0000.0000.000
88A86PRO00.0570.04438.2320.0020.0020.0000.0000.0000.000
89A87ASP-1-0.839-0.92541.146-0.078-0.0780.0000.0000.0000.000
90A88ASP-1-0.946-0.97944.361-0.079-0.0790.0000.0000.0000.000
91A89GLY00.0160.02042.3600.0020.0020.0000.0000.0000.000
92A90LEU0-0.032-0.01343.4170.0030.0030.0000.0000.0000.000
93A91THR00.0890.03540.221-0.002-0.0020.0000.0000.0000.000
94A92LEU00.0270.00442.1080.0040.0040.0000.0000.0000.000
95A93HIS0-0.043-0.03143.6980.0030.0030.0000.0000.0000.000
96A94ARG10.8470.91542.9980.0780.0780.0000.0000.0000.000
97A95LEU00.0240.02446.5340.0020.0020.0000.0000.0000.000
98A96SER0-0.015-0.02948.0300.0030.0030.0000.0000.0000.000
99A97GLY00.0520.02649.7340.0030.0030.0000.0000.0000.000
100A98PHE0-0.015-0.01548.7040.0020.0020.0000.0000.0000.000
101A99LEU0-0.003-0.00251.3330.0020.0020.0000.0000.0000.000
102A100ALA00.0180.02254.0570.0020.0020.0000.0000.0000.000
103A101ARG10.7560.85355.5510.0430.0430.0000.0000.0000.000
104A102TYR00.0090.00656.7160.0020.0020.0000.0000.0000.000
105A103LEU0-0.022-0.01757.7610.0020.0020.0000.0000.0000.000
106A104LEU0-0.0060.00660.0470.0010.0010.0000.0000.0000.000
107A105GLU-1-0.746-0.83760.528-0.038-0.0380.0000.0000.0000.000
108A106LYS10.8710.92161.6960.0340.0340.0000.0000.0000.000
109A107MET0-0.019-0.00964.1080.0010.0010.0000.0000.0000.000
110A108LEU0-0.0030.01365.9880.0010.0010.0000.0000.0000.000
111A109LYS10.8830.94765.9470.0300.0300.0000.0000.0000.000
112A110VAL0-0.057-0.00966.9180.0000.0000.0000.0000.0000.000
113A111SER00.0730.02969.9790.0010.0010.0000.0000.0000.000
114A112GLU-1-0.771-0.88171.775-0.022-0.0220.0000.0000.0000.000
115A113PRO00.0270.00472.4480.0000.0000.0000.0000.0000.000
116A114GLU-1-0.828-0.89366.786-0.028-0.0280.0000.0000.0000.000
117A115LYS10.8540.90867.8760.0220.0220.0000.0000.0000.000
118A116LEU00.0120.01567.8350.0000.0000.0000.0000.0000.000
119A117ILE00.0020.02765.4980.0000.0000.0000.0000.0000.000
120A118ILE0-0.028-0.01862.4830.0000.0000.0000.0000.0000.000
121A119LYS10.8340.89563.5120.0220.0220.0000.0000.0000.000
122A120SER0-0.041-0.01465.7280.0010.0010.0000.0000.0000.000
123A121LYS10.7990.89361.5480.0250.0250.0000.0000.0000.000
124A122ILE0-0.0060.00257.8870.0000.0000.0000.0000.0000.000
125A123ILE00.0310.02457.9150.0010.0010.0000.0000.0000.000
126A124ASN00.0400.00155.351-0.002-0.0020.0000.0000.0000.000
127A125PRO0-0.025-0.01752.8690.0010.0010.0000.0000.0000.000
128A126LEU0-0.018-0.00150.2830.0010.0010.0000.0000.0000.000
129A127ALA00.0280.03654.3810.0010.0010.0000.0000.0000.000
130A128GLU-1-0.747-0.85558.106-0.018-0.0180.0000.0000.0000.000
131A129LYS10.7190.87153.8400.0160.0160.0000.0000.0000.000
132A130ASN0-0.041-0.04354.6620.0020.0020.0000.0000.0000.000
133A131GLY0-0.006-0.00658.6170.0010.0010.0000.0000.0000.000
134A132ILE0-0.0030.03460.9770.0000.0000.0000.0000.0000.000
135A133THR0-0.001-0.03461.666-0.001-0.0010.0000.0000.0000.000
136A134TRP00.013-0.03861.481-0.001-0.0010.0000.0000.0000.000
137A135ASN0-0.041-0.01765.4800.0000.0000.0000.0000.0000.000
138A136ASP-1-0.804-0.88465.336-0.018-0.0180.0000.0000.0000.000
139A137GLY00.0470.03767.1930.0000.0000.0000.0000.0000.000
140A138GLU-1-0.821-0.91864.312-0.024-0.0240.0000.0000.0000.000
141A139GLU-1-0.834-0.90362.691-0.027-0.0270.0000.0000.0000.000
142A140VAL00.0390.03761.444-0.001-0.0010.0000.0000.0000.000
143A141TYR0-0.049-0.04560.294-0.001-0.0010.0000.0000.0000.000
144A142LEU0-0.013-0.00958.437-0.001-0.0010.0000.0000.0000.000
145A143SER0-0.013-0.03256.851-0.001-0.0010.0000.0000.0000.000
146A144PHE00.0110.01655.652-0.001-0.0010.0000.0000.0000.000
147A145PHE0-0.067-0.01052.8080.0000.0000.0000.0000.0000.000
148A146PRO0-0.0140.00047.980-0.001-0.0010.0000.0000.0000.000
149A147GLY00.0440.01749.569-0.001-0.0010.0000.0000.0000.000
150A148SER0-0.026-0.02550.242-0.001-0.0010.0000.0000.0000.000
151A149GLU-1-0.724-0.85349.237-0.047-0.0470.0000.0000.0000.000
152A150MET0-0.082-0.02549.065-0.002-0.0020.0000.0000.0000.000
153A151PHE00.0270.01052.167-0.001-0.0010.0000.0000.0000.000
154A152LEU00.0020.00754.7690.0020.0020.0000.0000.0000.000
155A153GLY00.0160.00057.6500.0020.0020.0000.0000.0000.000
156A154THR00.0130.00359.3820.0010.0010.0000.0000.0000.000
157A155PHE0-0.035-0.01756.2220.0010.0010.0000.0000.0000.000
158A156ARG10.8740.91560.5830.0270.0270.0000.0000.0000.000
159A157PHE00.0490.01358.8620.0010.0010.0000.0000.0000.000
160A158TYR00.0390.02559.4770.0000.0000.0000.0000.0000.000
161A159PRO0-0.014-0.00254.7370.0010.0010.0000.0000.0000.000
162A160LEU0-0.016-0.00454.9180.0000.0000.0000.0000.0000.000
163A161ALA00.0070.01956.4740.0010.0010.0000.0000.0000.000
164A162ILE00.0070.00555.5390.0010.0010.0000.0000.0000.000
165A163GLY00.013-0.00553.9650.0010.0010.0000.0000.0000.000
166A164ILE00.014-0.00554.6230.0010.0010.0000.0000.0000.000
167A165TYR0-0.019-0.01156.8630.0020.0020.0000.0000.0000.000
168A166LYS10.8210.90053.1420.0230.0230.0000.0000.0000.000
169A167VAL0-0.031-0.01851.5480.0010.0010.0000.0000.0000.000
170A168GLN0-0.028-0.00554.1020.0020.0020.0000.0000.0000.000
171A169ARG10.8040.90457.0850.0170.0170.0000.0000.0000.000
172A170LYS10.9320.96153.5890.0110.0110.0000.0000.0000.000
173A171GLU-1-0.807-0.87452.660-0.016-0.0160.0000.0000.0000.000
174A172MET0-0.047-0.01949.562-0.001-0.0010.0000.0000.0000.000
175A173GLU-1-0.765-0.85943.910-0.029-0.0290.0000.0000.0000.000
176A174PRO00.0530.00248.235-0.002-0.0020.0000.0000.0000.000
177A175LYS10.9130.96040.7980.0350.0350.0000.0000.0000.000
178A176TYR0-0.076-0.05543.217-0.004-0.0040.0000.0000.0000.000
179A177LEU0-0.0050.00547.161-0.001-0.0010.0000.0000.0000.000
180A178GLU-1-0.858-0.91443.348-0.052-0.0520.0000.0000.0000.000
181A179LYS10.8180.91045.4950.0520.0520.0000.0000.0000.000
182A180THR00.0420.01047.315-0.002-0.0020.0000.0000.0000.000
183A181MET0-0.006-0.00250.2410.0000.0000.0000.0000.0000.000
184A182ARG10.8610.92342.7170.0570.0570.0000.0000.0000.000
185A183GLN0-0.021-0.01247.962-0.004-0.0040.0000.0000.0000.000
186A184ARG10.8570.90850.1080.0570.0570.0000.0000.0000.000
187A185TYR00.0050.00755.3320.0010.0010.0000.0000.0000.000
188A186MET00.0300.01158.9710.0000.0000.0000.0000.0000.000
189A187GLY0-0.009-0.00858.538-0.001-0.0010.0000.0000.0000.000
190A188LEU0-0.0420.00258.425-0.001-0.0010.0000.0000.0000.000
191A189GLU-1-0.727-0.85752.880-0.052-0.0520.0000.0000.0000.000
192A190ALA00.0480.02252.7350.0020.0020.0000.0000.0000.000
193A191ALA00.0190.02754.8210.0020.0020.0000.0000.0000.000
194A192THR0-0.019-0.01756.4890.0020.0020.0000.0000.0000.000
195A193TRP0-0.027-0.02654.6820.0030.0030.0000.0000.0000.000
196A194THR0-0.050-0.03956.9190.0020.0020.0000.0000.0000.000
197A195VAL00.0270.00959.3010.0010.0010.0000.0000.0000.000
198A196SER0-0.0290.00462.8040.0010.0010.0000.0000.0000.000
199A197LYS10.8230.87662.7740.0290.0290.0000.0000.0000.000
200A198LEU00.0240.03762.4340.0000.0000.0000.0000.0000.000
201A199THR00.042-0.00764.0700.0010.0010.0000.0000.0000.000
202A200GLU-1-0.773-0.85465.092-0.026-0.0260.0000.0000.0000.000
203A201VAL00.0100.02060.3290.0000.0000.0000.0000.0000.000
204A202GLN0-0.021-0.00863.2260.0010.0010.0000.0000.0000.000
205A203SER0-0.054-0.01565.8210.0010.0010.0000.0000.0000.000
206A204ALA00.0490.01762.8320.0010.0010.0000.0000.0000.000
207A205LEU0-0.017-0.02261.6340.0000.0000.0000.0000.0000.000
208A206THR0-0.009-0.01963.7420.0010.0010.0000.0000.0000.000
209A207VAL00.0110.02066.2230.0010.0010.0000.0000.0000.000
210A208VAL00.000-0.00861.1670.0010.0010.0000.0000.0000.000
211A209SER0-0.071-0.04464.1870.0010.0010.0000.0000.0000.000
212A210SER0-0.022-0.01665.1200.0010.0010.0000.0000.0000.000
213A211LEU0-0.018-0.00164.0010.0010.0010.0000.0000.0000.000
214A212GLY0-0.0020.01766.1590.0000.0000.0000.0000.0000.000
215A213TRP0-0.014-0.02257.3990.0000.0000.0000.0000.0000.000
216A214LYS10.8670.95761.0360.0130.0130.0000.0000.0000.000
217A215LYS10.9690.98955.2460.0100.0100.0000.0000.0000.000
218A216THR00.015-0.00557.6730.0000.0000.0000.0000.0000.000
219A217ASN00.0570.01156.4530.0000.0000.0000.0000.0000.000
220A218VAL00.0050.01960.1020.0000.0000.0000.0000.0000.000
221A219SER00.0610.02363.259-0.001-0.0010.0000.0000.0000.000
222A220ALA00.0680.02666.8740.0000.0000.0000.0000.0000.000
223A221ALA00.0680.02769.3440.0000.0000.0000.0000.0000.000
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